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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 8-42838183-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=42838183&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 18,
"criteria": [
"PP2",
"BP4_Moderate",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "THAP1",
"hgnc_id": 20856,
"hgvs_c": "c.421G>A",
"hgvs_p": "p.Asp141Asn",
"inheritance_mode": "AD,SD",
"pathogenic_score": 1,
"score": -17,
"transcript": "NM_018105.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "PP2,BP4_Moderate,BP6_Very_Strong,BS1,BS2",
"acmg_score": -17,
"allele_count_reference_population": 131,
"alphamissense_prediction": null,
"alphamissense_score": 0.9085,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.13,
"chr": "8",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": "Multiple mitochondrial dysfunctions syndrome 9b,Torsion dystonia 6,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.07263758778572083,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 213,
"aa_ref": "D",
"aa_start": 141,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2161,
"cdna_start": 652,
"cds_end": null,
"cds_length": 642,
"cds_start": 421,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_018105.3",
"gene_hgnc_id": 20856,
"gene_symbol": "THAP1",
"hgvs_c": "c.421G>A",
"hgvs_p": "p.Asp141Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000254250.7",
"protein_coding": true,
"protein_id": "NP_060575.1",
"strand": false,
"transcript": "NM_018105.3",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 213,
"aa_ref": "D",
"aa_start": 141,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2161,
"cdna_start": 652,
"cds_end": null,
"cds_length": 642,
"cds_start": 421,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000254250.7",
"gene_hgnc_id": 20856,
"gene_symbol": "THAP1",
"hgvs_c": "c.421G>A",
"hgvs_p": "p.Asp141Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_018105.3",
"protein_coding": true,
"protein_id": "ENSP00000254250.3",
"strand": false,
"transcript": "ENST00000254250.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 53,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1943,
"cdna_start": null,
"cds_end": null,
"cds_length": 162,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000345117.2",
"gene_hgnc_id": 20856,
"gene_symbol": "THAP1",
"hgvs_c": "c.*63G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000344966.2",
"strand": false,
"transcript": "ENST00000345117.2",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 191,
"aa_ref": "D",
"aa_start": 119,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2108,
"cdna_start": 599,
"cds_end": null,
"cds_length": 576,
"cds_start": 355,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000934698.1",
"gene_hgnc_id": 20856,
"gene_symbol": "THAP1",
"hgvs_c": "c.355G>A",
"hgvs_p": "p.Asp119Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604757.1",
"strand": false,
"transcript": "ENST00000934698.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 117,
"aa_ref": "D",
"aa_start": 106,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 461,
"cdna_start": 423,
"cds_end": null,
"cds_length": 354,
"cds_start": 316,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000529779.1",
"gene_hgnc_id": 20856,
"gene_symbol": "THAP1",
"hgvs_c": "c.316G>A",
"hgvs_p": "p.Asp106Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000433912.1",
"strand": false,
"transcript": "ENST00000529779.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 53,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1965,
"cdna_start": null,
"cds_end": null,
"cds_length": 162,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_199003.2",
"gene_hgnc_id": 20856,
"gene_symbol": "THAP1",
"hgvs_c": "c.*63G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_945354.1",
"strand": false,
"transcript": "NM_199003.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 115,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1867,
"cdna_start": null,
"cds_end": null,
"cds_length": 348,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000934699.1",
"gene_hgnc_id": 20856,
"gene_symbol": "THAP1",
"hgvs_c": "c.268-141G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604758.1",
"strand": false,
"transcript": "ENST00000934699.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 113,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1330,
"cdna_start": null,
"cds_end": null,
"cds_length": 342,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000934700.1",
"gene_hgnc_id": 20856,
"gene_symbol": "THAP1",
"hgvs_c": "c.268-147G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604759.1",
"strand": false,
"transcript": "ENST00000934700.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs138345513",
"effect": "missense_variant",
"frequency_reference_population": 0.00008115968,
"gene_hgnc_id": 20856,
"gene_symbol": "THAP1",
"gnomad_exomes_ac": 69,
"gnomad_exomes_af": 0.0000471992,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 62,
"gnomad_genomes_af": 0.000407321,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "not specified|Torsion dystonia 6|Multiple mitochondrial dysfunctions syndrome 9b",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 6.774,
"pos": 42838183,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.461,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_018105.3"
}
]
}